The rheological properties of a cell suspension may play an important role in the flow field generated by populations of swimming micro-organisms (e.g. in bioconvection). In this paper, a swimming micro-organism is modelled as a squirming sphere with prescribed tangential surface velocity, in which the centre of mass of the sphere may be displaced from the geometric centre (bottom-heaviness). Effects of inertia and Brownian motion are neglected, because real micro-organisms swim at very low Reynolds numbers but are too large for Brownian effects to be important. The three-dimensional movement of 64 identical squirmers in a simple shear flow field, contained in a cube with periodic boundary conditions, is dynamically computed, for random initial positions and orientations. The computation utilizes a database of pairwise interactions that has been constructed by the boundary element method. The restriction to pairwise additivity of forces is expected to be justified if the suspension is semi-dilute. The results for non-bottom-heavy squirmers show that the squirming does not have a direct influence on the apparent viscosity. However, it does change the probability density in configuration space, and thereby causes a slight decrease in the apparent viscosity at O(c2), where c is the volume fraction of spheres. In the case of bottom-heavy squirmers, on the other hand, the stresslet generated by the squirming motion directly contributes to the bulk stress at O(c), and the suspension shows strong non-Newtonian properties. When the background simple shear flow is directed vertically, the apparent viscosity of the semi-dilute suspension of bottom-heavy squirmers becomes smaller than that of inert spheres. When the shear flow is horizontal and varies with the vertical coordinate, on the other hand, the apparent viscosity becomes larger than that of inert spheres. In addition, significant normal stress differences appear for all relative orientations of gravity and the shear flow, in the case of bottom-heavy squirmers.